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#+TITLE: Installing GeneNetwork services
* Table of Contents :TOC:
- [[#introduction][Introduction]]
- [[#source-deployment][Source deployment]]
- [[#install-guix][Install guix]]
- [[#checkout-the-git-repositories][Checkout the git repositories]]
- [[#update-guix][Update guix]]
- [[#update-the-path][Update the path]]
- [[#install-gn2][Install GN2]]
- [[#run-gn2][Run GN2]]
- [[#run-mysql-server][Run MySQL server]]
- [[#source-deployment-and-other-information-on-reproducibility][Source deployment and other information on reproducibility]]
* Introduction
Large system deployments tend to get very complex. In this document we
explain the GeneNetwork deployment system which is based on GNU Guix
(see also Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]). The Guix system can be used to install
GN with all its files and dependencies.
The official installation path is via a GNU Guix installation from a
checked out version of the Guix package tree (this is required for
reproducibility).
* Source deployment
** Install guix
Deploying from source is also straightforward. Install GNU Guix using
a binary tar ball as described [[https://github.com/pjotrp/guix-notes][here]].
If it works you should be able to install a package with
: guix package -i hello
** Checkout the git repositories
Check out the two relevant guix and guix-bioinformatics git
repositories:
#+begin_src bash
cd ~
mkdir genenetwork
cd genenetwork
git clone https://github.com/genenetwork/guix-bioinformatics
git clone --recursive --branch gn-latest https://github.com/genenetwork/guix guix-gn-latest
cd guix-gn-latest
#+end_src bash
** Update guix
At some point you may decide to create, install and run a recent
version of the guix-daemon by compiling the guix repository. Follow
[[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix][these]] steps carefully.
** Update the path
Now make sure the guix update path is in line with ours
#+begin_src bash
mkdir -p ~/.config/guix
ln -s ~/genenetwork/guix-gn-latest ~/.config/guix/latest
#+end_src bash
** Install GN2
#+begin_src bash
export GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/
cd ~/genenetwork/guix-gn-latest
./pre-inst guix package -i genenetwork2
#+end_src bash
** Run GN2
#+begin_src bash
export PATH=~/.guix-profile/bin:$PATH
genenetwork2
#+end_src bash
will start the default server which listens on port 5003.
** Run MySQL server
At this point we require the underlying distribution to install
and run mysqld.
Download one of
http://files.genenetwork.org/raw_database/
https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip
Check the md5sum.
After installation inflate the database binary in the MySQL directory
(this is subject to change soon)
: chown -R mysql:mysql db_webqtl_s/
: chmod 700 db_webqtl_s/
: chmod 660 db_webqtl_s/*
restart MySQL service (mysqld). Login as root and
: mysql> show databases;
: +--------------------+
: | Database |
: +--------------------+
: | information_schema |
: | db_webqtl_s |
: | mysql |
: | performance_schema |
: +--------------------+
Set permissions and match password in your settings file below:
: mysql> grant all privileges on db_webqtl_s.* to gn2@"localhost" identified by 'mysql_password';
* Source deployment and other information on reproducibility
See the document [[GUIX-Reproducible-from-source.org]].
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